3CKZ

N1 Neuraminidase H274Y + Zanamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants.

Collins, P.J.Haire, L.F.Lin, Y.P.Liu, J.Russell, R.J.Walker, P.A.Skehel, J.J.Martin, S.R.Hay, A.J.Gamblin, S.J.

(2008) Nature 453: 1258-1261

  • DOI: 10.1038/nature06956
  • Primary Citation of Related Structures:  
    3CKZ, 3CL0, 3CL2

  • PubMed Abstract: 
  • The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles ...

    The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles. The principal target for these drugs is a virus surface glycoprotein, neuraminidase, which facilitates the release of nascent virus and thus the spread of infection. Oseltamivir (Tamiflu) and zanamivir (Relenza) are two currently used neuraminidase inhibitors that were developed using knowledge of the enzyme structure. It has been proposed that the closer such inhibitors resemble the natural substrate, the less likely they are to select drug-resistant mutant viruses that retain viability. However, there have been reports of drug-resistant mutant selection in vitro and from infected humans. We report here the enzymatic properties and crystal structures of neuraminidase mutants from H5N1-infected patients that explain the molecular basis of resistance. Our results show that these mutants are resistant to oseltamivir but still strongly inhibited by zanamivir owing to an altered hydrophobic pocket in the active site of the enzyme required for oseltamivir binding. Together with recent reports of the viability and pathogenesis of H5N1 (ref. 7) and H1N1 (ref. 8) viruses with neuraminidases carrying these mutations, our results indicate that it would be prudent for pandemic stockpiles of oseltamivir to be augmented by additional antiviral drugs, including zanamivir.


    Organizational Affiliation

    MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA385Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 1 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for Q6DPL2 (Influenza A virus)
Explore Q6DPL2 
Go to UniProtKB:  Q6DPL2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZMR
Query on ZMR

Download Ideal Coordinates CCD File 
C [auth A]ZANAMIVIR
C12 H20 N4 O7
ARAIBEBZBOPLMB-UFGQHTETSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZMRIC50:  2.9000000953674316   nM  BindingDB
ZMRIC50:  3.700000047683716   nM  BindingDB
ZMRIC50:  2.4000000953674316   nM  BindingDB
ZMRIC50:  2.200000047683716   nM  BindingDB
ZMRIC50:  2.700000047683716   nM  BindingDB
ZMRIC50:  5.900000095367432   nM  BindingDB
ZMRIC50:  7.400000095367432   nM  BindingDB
ZMRIC50:  0.28999999165534973   nM  BindingDB
ZMRIC50:  5.400000095367432   nM  BindingDB
ZMRIC50:  7.699999809265137   nM  BindingDB
ZMRIC50:  1.100000023841858   nM  BindingDB
ZMRIC50:  2.200000047683716   nM  BindingDB
ZMRIC50:  0.029999999329447746   nM  BindingDB
ZMRIC50:  1.600000023841858   nM  BindingDB
ZMRIC50:  6.699999809265137   nM  BindingDB
ZMRIC50:  1.100000023841858   nM  BindingDB
ZMRIC50:  0.20000000298023224   nM  BindingDB
ZMRIC50:  0.6000000238418579   nM  BindingDB
ZMRIC50:  5.099999904632568   nM  BindingDB
ZMRIC50:  18   nM  BindingDB
ZMRIC50:  23   nM  BindingDB
ZMRKi:  0.5   nM  BindingDB
ZMRIC50:  5.599999904632568   nM  BindingDB
ZMRIC50:  1.2000000476837158   nM  BindingDB
ZMRIC50:  0.800000011920929   nM  BindingDB
ZMRIC50:  2.299999952316284   nM  BindingDB
ZMRIC50:  10   nM  BindingDB
ZMRIC50:  11   nM  BindingDB
ZMRIC50:  1.899999976158142   nM  BindingDB
ZMRIC50:  12   nM  BindingDB
ZMRIC50:  1.7000000476837158   nM  BindingDB
ZMRIC50:  13   nM  BindingDB
ZMRIC50:  3.299999952316284   nM  BindingDB
ZMRIC50:  14   nM  BindingDB
ZMRIC50:  5.300000190734863   nM  BindingDB
ZMRIC50:  0.05000000074505806   nM  BindingDB
ZMRIC50:  2.4000000953674316   nM  BindingDB
ZMRIC50:  0.5799999833106995   nM  BindingDB
ZMRIC50:  3.4000000953674316   nM  BindingDB
ZMRKi:  1   nM  BindingDB
ZMRIC50:  8.100000381469727   nM  BindingDB
ZMRIC50:  1.399999976158142   nM  BindingDB
ZMRIC50:  4.800000190734863   nM  BindingDB
ZMRKi :  1.899999976158142   nM  PDBBind
ZMRIC50:  34   nM  BindingDB
ZMRIC50:  0.4699999988079071   nM  BindingDB
ZMRIC50:  40   nM  BindingDB
ZMRIC50:  1.2999999523162842   nM  BindingDB
ZMRIC50:  4.300000190734863   nM  BindingDB
ZMRIC50:  6.800000190734863   nM  BindingDB
ZMRIC50:  45   nM  BindingDB
ZMRIC50:  52   nM  BindingDB
ZMRIC50:  7.300000190734863   nM  BindingDB
ZMRIC50:  2.299999952316284   nM  BindingDB
ZMRIC50:  5.800000190734863   nM  BindingDB
ZMRKi:  1.600000023841858   nM  BindingDB
ZMRIC50:  0.699999988079071   nM  BindingDB
ZMRIC50:  1   nM  BindingDB
ZMRIC50:  7.699999809265137   nM  BindingDB
ZMRIC50:  9.100000381469727   nM  BindingDB
ZMRIC50:  7.800000190734863   nM  BindingDB
ZMRIC50:  8.600000381469727   nM  BindingDB
ZMRIC50:  0.8799999952316284   nM  BindingDB
ZMRIC50:  1.5   nM  BindingDB
ZMRIC50:  5   nM  BindingDB
ZMRIC50:  0.6000000238418579   nM  BindingDB
ZMRIC50:  0.75   nM  BindingDB
ZMRIC50:  2   nM  BindingDB
ZMRIC50:  0.800000011920929   nM  BindingDB
ZMRKi:  0.1899999976158142   nM  Binding MOAD
ZMRKi:  0.5   nM  BindingDB
ZMRIC50:  4   nM  BindingDB
ZMRIC50:  12   nM  BindingDB
ZMRIC50:  0.44999998807907104   nM  BindingDB
ZMRIC50:  5.5   nM  BindingDB
ZMRIC50:  6   nM  BindingDB
ZMRIC50:  6.5   nM  BindingDB
ZMRIC50:  2   nM  BindingDB
ZMRIC50:  9.199999809265137   nM  BindingDB
ZMRIC50:  0.03999999910593033   nM  BindingDB
ZMRIC50:  2.5   nM  BindingDB
ZMRIC50:  8.699999809265137   nM  BindingDB
ZMRIC50:  8.199999809265137   nM  BindingDB
ZMRIC50:  7.599999904632568   nM  BindingDB
ZMRIC50:  3   nM  BindingDB
ZMRIC50:  0.49000000953674316   nM  BindingDB
ZMRIC50:  3.5   nM  BindingDB
ZMRIC50:  5.199999809265137   nM  BindingDB
ZMRIC50:  1.399999976158142   nM  BindingDB
ZMRIC50:  1.7999999523162842   nM  BindingDB
ZMRIC50:  0.6600000262260437   nM  BindingDB
ZMRIC50:  1.559999942779541   nM  BindingDB
ZMRIC50:  1.7999999523162842   nM  BindingDB
ZMRIC50:  0.699999988079071   nM  BindingDB
ZMRIC50:  7.199999809265137   nM  BindingDB
ZMRIC50:  1.399999976158142   nM  BindingDB
ZMRIC50:  8.300000190734863   nM  BindingDB
ZMRIC50:  11   nM  BindingDB
ZMRIC50:  1   nM  BindingDB
ZMRIC50:  9.300000190734863   nM  BindingDB
ZMRIC50:  4.199999809265137   nM  BindingDB
ZMRIC50:  9.800000190734863   nM  BindingDB
ZMRIC50:  3.5999999046325684   nM  BindingDB
ZMRIC50:  3.0999999046325684   nM  BindingDB
ZMRIC50:  0.5   nM  BindingDB
ZMRIC50:  4.800000190734863   nM  BindingDB
ZMRIC50:  2.5999999046325684   nM  BindingDB
ZMRKi:  0.4000000059604645   nM  BindingDB
ZMRIC50:  2.0999999046325684   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.146α = 90
b = 115.146β = 90
c = 64.197γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations